At about age 5, Eleanor's daughter Anne Catherine became severely ill and nearly died. She contracted a high fever and her extremities began to swell. For two years she was ill. Finally Eleanor and William appealed to the Virgin Mary with deep prayer, promising to raise Anne as a child of Mary if she lived on. Soon Anne became healthy again. Eleanor and William told their daughter of the Virgin Mary's intervention on her behalf and the promise they had made. From there out Eleanor educated and guided Anne Catherine in the cultivation of devotion to Mary. Throughout childhood Anne Catherine displayed a consistent sense of piety.

Eleonora died on 5 August 1594 at the age of 59, she had been a widow since 1587 when her husband died. She was one of the last children of Ferdinand and Anna alive at the time, the only other sibling alive at the time of her death was her brother Ferdinand II, Archduke of Austria who only died one year later.